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Article
Open AccessSTARRPeaker: uniform processing and accurate identification of STARR-seq active regions
STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is...
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Article
Open AccessNIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis
Identifying frequently mutated regions is a key approach to discover DNA elements influencing cancer progression. However, it is challenging to identify these burdened regions due to mutation rate heterogeneit...
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Article
Open AccessRADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins
RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation and disease. Their binding sites cover more of the genome than coding exons; nevertheless, most noncoding variant prioritization me...
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Article
Open AccessDiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring
During transcription, numerous transcription factors (TFs) bind to targets in a highly coordinated manner to control the gene expression. Alterations in groups of TF-binding profiles (i.e. “co-binding changes”...